Modified nucleotides in the genome are associated with epigenetics in general and regulation of transcriptional activation in particular. Detection and/or mapping of modified nucleotides in the genome are important for the understanding of the relationship of phenotype to genotype. Examples of modified nucleotides are 5-hydroxymethylcytosine (5-hmC) and 5-methylated cytosine (5-mC). One approach to detection/mapping of these modified nucleotides is bisulfite sequencing. However, this technique cannot differentiate between the two forms. An alternative approach has been to use T4-β-glucosyltransferase (BGT) to transfer glucose from uridine diphospho-glucose (UDP-Glc) to 5-hmC. The glucose is amenable to chemical derivatization with an azide or thio group (US Published Application No: 2011/0236894 and International Published Application No: WO 2011/02581). Alternative substrates for BGT and other glycosyltransferases would prove useful for enhancing the sensitivity and specificity for 5-hmC and other modified nucleotides analysis as well as for multiplex analysis.